Martis
thank you very much for helping me to go through x leap
After editing I saved NADP.frcmod NADP.prepi NADP.pdb
but it gives warning 'dont forget to remove improper dihedrals'
what to do for this?
and will I load this pdb and frcmod file in generating .inprcd and prmtop
files for complex in tleap?
thank you
Sadaf
On Wed, Jun 26, 2019 at 5:53 AM Elvis Martis <elvis.martis.bcp.edu.in>
wrote:
> Hello
> Since you did not source the gaff force field, leap threw out those errors.
> Please use the following commands, (I am assuming you are using
> AmbertTools 17 or later)
> xleap
> source leaprc.protein.ff14SB (for protein)
> source leaprc.water.tip3p (for Tip3p waters and counterions)
> sourcc leaprc.gaff
> loadamberparams NADP.frcmod (check if the file name is correct and placed
> in the working directory)
> loadamberprep NADP.prepi
> list (this will show all residue names)
> edit XXX (enter the residue name, here enter the name for NADP)
>
>
> Best Regards
>
> Elvis Martis
>
>
>
> ________________________________
> From: Sadaf Rani <sadafrani6.gmail.com>
> Sent: 25 June 2019 21:59
> To: AMBER Mailing List
> Subject: Re: [AMBER] open valance problem
>
> Dear Martis
> I loaded frcmod & prepi files by using following commands:
>
> mods loadAmberParams NADP.frcmod
> mods2 loadAmberParams NADP.prepi
>
> it shows error as mentioed in screenshot.
>
> Kindly suggest me the right way
>
> thank you
>
> Sadaf
>
> On Tue, Jun 25, 2019 at 6:11 AM Elvis Martis <elvis.martis.bcp.edu.in>
> wrote:
>
> > Hello,
> > you really don't need to obtain the mol2 file this way.
> > I would suggest loading the frcmod and prepi files that you obtained from
> > the Manchester database in xleap.
> > Then see the residue name and atom names for NADP in the database and
> > according modify them in your PDB file (coordinates as complexed with the
> > protein). Once all atoms names and residue names are as per the prepi
> > file, leap should not throw any errors.
> >
> > Hope this helps
> >
> >
> > Best Regards
> >
> > Elvis Martis
> >
> >
> >
> > ________________________________
> > From: Sadaf Rani <sadafrani6.gmail.com>
> > Sent: 25 June 2019 01:55
> > To: AMBER Mailing List
> > Subject: Re: [AMBER] open valance problem
> >
> > Dear Elvis
> >
> > I looked for the NADP parameters as you suggested but I want to get the
> > mol2 file from the same process to loads in to t leap for parameter
> > generation
> > as commands below:-
> >
> > source leaprc.protein.ff14SB
> > source leaprc.gaff2
> > source leaprc.water.tip3p
> >
> > ligA = loadmol2 NAP_amber.mol2
> > ligB = loadmol2 BG6_amber.mol2
> >
> > loadamberparams NAP_amber.frcmod
> > loadamberparams BG6_amber.frcmod
> >
> >
> > protein = loadPdb "Combined_nolig.pdb"
> > complex = combine {protein ligA ligB}
> > protein = createUnit Combined_nolig.pdb
> > setBox protein "vdw"
> > solvateBox protein TIP3PBOX 14.0 iso
> > addIonsRand complex Na+ 0
> > saveamberparm complex complex.prmtop complex.inpcrd
> > quit
> >
> >
> > but when I try
> >
> > antechamber -i NADP_1.pdb -fi pdb -o NADP_1.mol2 -fo mol2 -c bcc -pf yes
> > -nc -3 -m 1 -at gaff2 -j 4
> >
> > it gives error
> >
> > Welcome to antechamber: molecular input file processor.
> >
> > acdoctor mode is on: check and diagnosis problems in the input file.
> > -- Check Format for pdb File --
> > Status: pass
> > -- Check Unusual Elements --
> > Status: pass
> > -- Check Open Valences --
> > Status: pass
> > -- Check Geometry --
> > for those bonded
> > for those not bonded
> > Status: pass
> > -- Check Weird Bonds --
> > Status: pass
> > -- Check Number of Units --
> > Status: pass
> > acdoctor mode has completed checking the input file.
> >
> > Info: Bond types are assigned for valence state (1) with penalty (1).
> > Info: Total number of electrons: 384; net charge: -3
> >
> > Running: /home/srania/Amber/amber16/bin/sqm -O -i sqm.in -o sqm.out
> > /home/srania/Amber/amber16/bin/to_be_dispatched/antechamber: Fatal Error!
> > Cannot properly run "/home/srania/Amber/amber16/bin/sqm -O -i sqm.in -o
> > sqm.out".
> >
> > How can I solve this error
> > How can I calculate the parameters for NADP+ if I want to learn at my
> own
> >
> >
> > will be really thankful for answer
> >
> > thank you
> > Sadaf
> >
> >
> > On Sun, Jun 23, 2019 at 4:57 AM Elvis Martis <elvis.martis.bcp.edu.in>
> > wrote:
> >
> > > Hello
> > > NADP parameters are already available
> > > http://research.bmh.manchester.ac.uk/bryce/amber/.
> > >
> > >
> > > Best Regards
> > >
> > > Elvis Martis
> > >
> > >
> > >
> > > ________________________________
> > > From: Sadaf Rani <sadafrani6.gmail.com>
> > > Sent: 22 June 2019 18:56
> > > To: AMBER Mailing List
> > > Subject: [AMBER] open valance problem
> > >
> > > Dear Amber
> > > I am trying to find to parameters for co-factor NADP+ by antechamber
> > > But when I use this command:-
> > > antechamber -i NADP_noH.mol2 -fi mol2 -o NADP_amber.mol2 -fo mol2 -c
> bcc
> > > -pf yes -nc -3 -at gaff2 -j 4
> > >
> > > It gives me this error
> > >
> > > Welcome to antechamber: molecular input file processor.
> > >
> > > acdoctor mode is on: check and diagnosis problems in the input file.
> > > -- Check Format for mol2 File --
> > > Status: pass
> > > -- Check Unusual Elements --
> > > Status: pass
> > > -- Check Open Valences --
> > > Warning: The number of bonds (1) for atom (ID: 33, Name: O1N) does not
> > > match
> > > the connectivity (2) for atom type (O.3) defined in
> > > CORR_NAME_TYPE.DAT.
> > > Warning: The number of bonds (1) for atom (ID: 34, Name: O1X) does not
> > > match
> > > the connectivity (2) for atom type (O.3) defined in
> > > CORR_NAME_TYPE.DAT.
> > > Warning: The number of bonds (1) for atom (ID: 39, Name: O2A) does not
> > > match
> > > the connectivity (2) for atom type (O.3) defined in
> > > CORR_NAME_TYPE.DAT.
> > > Warning: The number of bonds (1) for atom (ID: 43, Name: O2X) does not
> > > match
> > > the connectivity (2) for atom type (O.3) defined in
> > > CORR_NAME_TYPE.DAT.
> > > Warning: The number of bonds (3) for atom (ID: 55, Name: C4N) does not
> > > match
> > > the connectivity (4) for atom type (C.3) defined in
> > > CORR_NAME_TYPE.DAT.
> > > Warning: The number of bonds (3) for atom (ID: 72, Name: N9A) does not
> > > match
> > > the connectivity (2) for atom type (N.ar) defined in
> > > CORR_NAME_TYPE.DAT.
> > > But, you may safely ignore the warnings if your molecule
> > > uses atom names or element names as atom types.
> > > -- Check Geometry --
> > > for those bonded
> > > for those not bonded
> > > Status: pass
> > > -- Check Weird Bonds --
> > > /home/srania/Amber/amber16/bin/to_be_dispatched/antechamber: Fatal
> Error!
> > > Weird atomic valence (3) for atom (ID: 55, Name: C4N).
> > > Possible open valence.
> > >
> > > Hoe to solve this issue
> > > I have attached .mol2 file if there is something wrong please tell me.
> > >
> > > thank you in advance
> > > _______________________________________________
> > > AMBER mailing list
> > > AMBER.ambermd.org
> > > http://lists.ambermd.org/mailman/listinfo/amber
> > >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
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Received on Wed Jun 26 2019 - 15:00:02 PDT
